Magnesium in PDB 5wsb: Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Allosteric Activators Amp and Glucose 6-Phosphate

Enzymatic activity of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Allosteric Activators Amp and Glucose 6-Phosphate

All present enzymatic activity of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Allosteric Activators Amp and Glucose 6-Phosphate:
2.7.1.40;

Protein crystallography data

The structure of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Allosteric Activators Amp and Glucose 6-Phosphate, PDB code: 5wsb was solved by W.Zhong, Q.Cai, A.El Sahili, J.Lescar, P.C.Dedon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.82 / 2.25
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 125.631, 125.631, 144.514, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 22.8

Other elements in 5wsb:

The structure of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Allosteric Activators Amp and Glucose 6-Phosphate also contains other interesting chemical elements:

Potassium (K) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Allosteric Activators Amp and Glucose 6-Phosphate (pdb code 5wsb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Allosteric Activators Amp and Glucose 6-Phosphate, PDB code: 5wsb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5wsb

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Magnesium binding site 1 out of 4 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Allosteric Activators Amp and Glucose 6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Allosteric Activators Amp and Glucose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:32.9
occ:1.00
 O A:HOH633 2.0 23.8 1.0
O A:HOH636 2.0 30.8 1.0
O4 A:OXL504 2.1 30.0 1.0
OD2 A:ASP244 2.1 34.0 1.0
OE1 A:GLU220 2.1 29.8 1.0
O3 A:OXL504 2.2 23.1 1.0
C2 A:OXL504 2.9 29.3 1.0
C1 A:OXL504 2.9 31.1 1.0
CD A:GLU220 3.1 32.9 1.0
CG A:ASP244 3.2 31.9 1.0
OE2 A:GLU220 3.4 28.4 1.0
NZ A:LYS218 3.7 31.3 1.0
CB A:ASP244 3.8 30.5 1.0
O2 A:OXL504 4.1 25.2 1.0
O1 A:OXL504 4.2 23.6 1.0
OD1 A:ASP244 4.2 31.3 1.0
CE A:LYS218 4.3 32.0 1.0
CG A:GLU220 4.5 33.5 1.0
CZ A:PHE192 4.5 32.9 1.0
N A:ASP244 4.6 32.4 1.0
CB A:ALA241 4.6 31.6 1.0
OG A:SER191 4.7 32.8 1.0
CE1 A:PHE192 4.8 31.5 1.0
CB A:GLU220 4.8 34.6 1.0
CA A:ASP244 4.9 33.0 1.0
CE2 A:PHE192 5.0 32.4 1.0

Magnesium binding site 2 out of 4 in 5wsb

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Magnesium binding site 2 out of 4 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Allosteric Activators Amp and Glucose 6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Allosteric Activators Amp and Glucose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:35.2
occ:1.00
 O2 B:OXL504 2.0 26.5 1.0
OD2 B:ASP244 2.0 37.6 1.0
O B:HOH625 2.1 27.3 1.0
O1 B:OXL504 2.2 22.0 1.0
O B:HOH660 2.2 21.7 1.0
OE1 B:GLU220 2.3 33.2 1.0
C2 B:OXL504 2.7 32.0 1.0
C1 B:OXL504 2.8 30.1 1.0
CG B:ASP244 3.2 33.9 1.0
CD B:GLU220 3.3 35.4 1.0
OE2 B:GLU220 3.5 34.2 1.0
CB B:ASP244 3.8 31.4 1.0
NZ B:LYS218 3.9 30.5 1.0
O4 B:OXL504 4.0 29.9 1.0
O3 B:OXL504 4.0 25.2 1.0
OD1 B:ASP244 4.2 35.9 1.0
O B:HOH642 4.3 19.2 1.0
CZ B:PHE192 4.3 31.8 1.0
CE B:LYS218 4.6 31.0 1.0
N B:ASP244 4.7 32.4 1.0
CG B:GLU220 4.7 34.3 1.0
CE1 B:PHE192 4.7 30.7 1.0
CE2 B:PHE192 4.8 32.5 1.0
OG B:SER191 4.8 31.6 1.0
CA B:ASP244 4.9 33.2 1.0
CB B:ALA241 5.0 31.7 1.0

Magnesium binding site 3 out of 4 in 5wsb

Go back to Magnesium Binding Sites List in 5wsb
Magnesium binding site 3 out of 4 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Allosteric Activators Amp and Glucose 6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Allosteric Activators Amp and Glucose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:32.3
occ:1.00
 OD2 C:ASP244 1.9 39.1 1.0
O C:HOH630 1.9 28.2 1.0
O C:HOH606 2.0 27.2 1.0
OE1 C:GLU220 2.2 33.0 1.0
O2 C:OXL504 2.3 29.3 1.0
O1 C:OXL504 2.5 29.7 1.0
CG C:ASP244 3.0 36.4 1.0
C2 C:OXL504 3.1 27.9 1.0
C1 C:OXL504 3.1 29.9 1.0
CD C:GLU220 3.2 32.1 1.0
OE2 C:GLU220 3.5 29.6 1.0
CB C:ASP244 3.6 36.6 1.0
OD1 C:ASP244 4.0 32.8 1.0
NZ C:LYS218 4.1 31.5 1.0
O4 C:OXL504 4.2 24.3 1.0
N C:ASP244 4.3 36.8 1.0
O3 C:OXL504 4.3 26.1 1.0
NZ C:LYS72 4.4 52.4 1.0
CZ C:PHE192 4.4 38.3 1.0
CG C:GLU220 4.6 32.1 1.0
CE C:LYS218 4.6 32.2 1.0
CA C:ASP244 4.6 35.4 1.0
CB C:ALA241 4.6 29.3 1.0
CE1 C:PHE192 4.7 38.2 1.0
CB C:GLU220 4.8 34.4 1.0
CE2 C:PHE192 4.9 40.5 1.0
OG C:SER191 5.0 31.1 1.0

Magnesium binding site 4 out of 4 in 5wsb

Go back to Magnesium Binding Sites List in 5wsb
Magnesium binding site 4 out of 4 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Allosteric Activators Amp and Glucose 6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Allosteric Activators Amp and Glucose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:30.8
occ:1.00
 OD2 D:ASP244 1.8 39.6 1.0
O1 D:OXL504 1.9 26.9 1.0
OE1 D:GLU220 1.9 34.0 1.0
O D:HOH652 2.2 23.8 1.0
O D:HOH640 2.3 23.6 1.0
O2 D:OXL504 2.5 29.9 1.0
C1 D:OXL504 2.8 29.1 1.0
CG D:ASP244 2.9 37.0 1.0
CD D:GLU220 3.0 33.1 1.0
C2 D:OXL504 3.1 30.0 1.0
CB D:ASP244 3.4 37.3 1.0
OE2 D:GLU220 3.5 31.5 1.0
OD1 D:ASP244 4.0 37.3 1.0
O3 D:OXL504 4.0 24.9 1.0
N D:ASP244 4.1 38.5 1.0
CG D:GLU220 4.3 34.0 1.0
O4 D:OXL504 4.3 29.2 1.0
CA D:ASP244 4.4 37.6 1.0
NZ D:LYS218 4.4 29.2 1.0
CZ D:PHE192 4.4 39.4 1.0
CB D:ALA241 4.5 29.5 1.0
CB D:GLU220 4.5 34.0 1.0
CE1 D:PHE192 4.6 39.5 1.0
CE D:LYS218 4.8 29.6 1.0
O D:HOH649 4.8 34.3 1.0
O D:HOH637 4.9 26.2 1.0
CE2 D:PHE192 4.9 41.3 1.0

Reference:

W.Zhong, L.Cui, B.C.Goh, Q.Cai, P.Ho, Y.H.Chionh, M.Yuan, A.E.Sahili, L.A.Fothergill-Gilmore, M.D.Walkinshaw, J.Lescar, P.C.Dedon. Allosteric Pyruvate Kinase-Based "Logic Gate" Synergistically Senses Energy and Sugar Levels in Mycobacterium Tuberculosis. Nat Commun V. 8 1986 2017.
ISSN: ESSN 2041-1723
PubMed: 29215013
DOI: 10.1038/S41467-017-02086-Y
Page generated: Mon Dec 14 21:24:56 2020

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